2017 dials.stills process - Revision history

Aaron at 00:11, 2 March 2017

2017-03-02T00:11:23Z

← Older revision		Revision as of 00:11, 2 March 2017
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	~~Processing~~ the example data from DLS (Credit: Danny Axford). Pilatus data, 11000 images. For the sake of this example, we will be in a folder named $work, and the images are in a folder named $data		Here we give the commands for processing the example data from DLS (Credit: Danny Axford). These data are Pilatus data, 11000 images, but these commands are generally applicable for processing stills using dials.stills_process. For the sake of this example, we will be in a folder named $work, and the images are in a folder named $data

	Remember, all these commands have ~~great~~ help strings, use -h, or to see details for the parameters, use -c. If you want to see all the parameters, use -e 10. And if you want to see the descriptions of each parameters, use -a 2. Example:		Remember, all these commands have help strings, use -h, or to see details for the parameters, use -c. If you want to see all the parameters, use -e 10. And if you want to see the descriptions of each parameters, use -a 2. Example:
	dials.import -c -a 2 -e 10 \| less		dials.import -c -a 2 -e 10 \| less

Aaron at 00:07, 2 March 2017

2017-03-02T00:07:23Z

← Older revision		Revision as of 00:07, 2 March 2017
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	dxtbx.plot_detector_models combined_experiments.json refined_experiments.json		dxtbx.plot_detector_models combined_experiments.json refined_experiments.json

	We can reprocess all the data using this updated geometry, y adding this to the process.phil		We can reprocess all the data using this updated geometry, adding this to the process.phil
	input.reference_geometry=$work/metrology/refined_experiments.json		input.reference_geometry=$work/metrology/refined_experiments.json

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	From here, proceed to merging:		From here, proceed to merging:

	~~(link to mona’s merging on wiki)~~		[[2017_prime_tutorial \| PRIME]]

Aaron at 00:02, 2 March 2017

2017-03-02T00:02:35Z

@@ Line 1: / Line 1: @@
-Phil file for today:
+Processing the example data from DLS (Credit: Danny Axford).  Pilatus data, 11000 images.  For the sake of this example, we will be in a folder named $work, and the images are in a folder named $data
 <pre>
-spotfinder.lookup.mask=/net/dials/raid1/aaron/zurich0038/mask2.pickle
+spotfinder.lookup.mask=$work/averages/mask.pickle
 spotfinder.filter.min_spot_size=2
 verbosity=10
 indexing {
@@ Line 11: / Line 35: @@
      unit_cell = 91.7 91.7 46 90 90 120
+   }
    refinement_protocol.n_macro_cycles = 1
    refinement_protocol.d_min_start=2.0
@@ Line 19: / Line 41: @@
    stills.method_list=fft1d real_space_grid_search
+}
 verbosity=10
 integration {
@@ Line 56: / Line 77: @@
+}
 </pre>

Aaron: Created page with "Phil file for today:

 spotfinder.lookup.mask=/net/dials/raid1/aaron/zurich0038/mask2.pickle spotfinder.filter.min_spot_size=2 integration.lookup.mask=/net/dials/raid1/a..."

2017-02-17T18:08:38Z

Created page with "Phil file for today: <pre> spotfinder.lookup.mask=/net/dials/raid1/aaron/zurich0038/mask2.pickle spotfinder.filter.min_spot_size=2 integration.lookup.mask=/net/dials/raid1/a..."

New page

Phil file for today:

<pre>
spotfinder.lookup.mask=/net/dials/raid1/aaron/zurich0038/mask2.pickle
spotfinder.filter.min_spot_size=2
integration.lookup.mask=/net/dials/raid1/aaron/zurich0038/mask2.pickle
verbosity=10
indexing {
known_symmetry {
space_group = P6
unit_cell = 91.7 91.7 46 90 90 120
}
#method=fft1d
#method=real_space_grid_search
refinement_protocol.n_macro_cycles = 1
refinement_protocol.d_min_start=2.0
basis_vector_combinations.max_try=10
stills.indexer=stills
stills.method_list=fft1d real_space_grid_search
}

verbosity=10
integration {
integrator=stills
profile.fitting=False
background {
simple {
outlier {
algorithm = null
}
}
}
}
profile {
gaussian_rs {
min_spots.overall = 0
}
}

refinement {
parameterisation {
beam.fix=all
detector.fix=all
detector.hierarchy_level=0
auto_reduction {
action=fix
min_nref_per_parameter=1
}
treat_single_image_as_still=True
}
reflections {
outlier.algorithm=null
weighting_strategy.override=stills
weighting_strategy.delpsi_constant=1000000
}
}
</pre>